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1 <?xml version="1.0" ?>
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2 <tool id="qiime_alignment_mask" name="qiime alignment mask" version="2018.4">
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3 <description> - Positional conservation and gap filtering.</description>
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4 <requirements>
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5 <requirement type="package" version="2018.4">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8
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9 qiime alignment mask --i-alignment=$ialignment
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10
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11 #if str($cmdconfig) != 'None':
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12 --cmd-config=$cmdconfig
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13 #end if
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14
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15 --o-masked-alignment=omaskedalignment
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16
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17 #if $pminconservation:
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18 --p-min-conservation=$pminconservation
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19 #end if
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20
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21 #if $pmaxgapfrequency:
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22 --p-max-gap-frequency=$pmaxgapfrequency
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23 #end if
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24 ;
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25 cp omaskedalignment.qza $omaskedalignment
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26
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27 ]]></command>
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28 <inputs>
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29 <param format="qza,no_unzip.zip" label="--i-alignment: FeatureData[AlignedSequence] - The alignment to be masked. [required]" name="ialignment" optional="False" type="data"/>
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30 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
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31 <param label="--p-min-conservation: The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences. [default: 0.4]" name="pminconservation" optional="True" type="float" value="0.4"/>
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32 <param label="--p-max-gap-frequency: The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency. [default: 1.0]" name="pmaxgapfrequency" optional="True" type="float" value="1.0"/>
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33 </inputs>
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34 <outputs>
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35 <data format="qza" label="${tool.name} on ${on_string}: maskedalignment.qza" name="omaskedalignment"/>
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36 </outputs>
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37 <help><![CDATA[
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38
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39 Positional conservation and gap filtering.
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40 ------------------------------------------
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41
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42 Mask (i.e., filter) unconserved and highly gapped columns from an
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43 alignment.
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44
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45 Parameters
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46 ----------
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47 alignment : FeatureData[AlignedSequence]
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48 The alignment to be masked.
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49 max_gap_frequency : Float, optional
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50 The maximum relative frequency of gap characters in a column for the
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51 column to be retained. This relative frequency must be a number between
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52 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without
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53 gap characters, and 1.0 retains all columns regardless of gap character
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54 frequency.
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55 min_conservation : Float, optional
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56 The minimum relative frequency of at least one non-gap character in a
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57 column for that column to be retained. This relative frequency must be
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58 a number between 0.0 and 1.0 (inclusive). For example, if a value of
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59 0.4 is provided, a column will only be retained if it contains at least
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60 one character that is present in at least 40% of the sequences.
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61
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62 Returns
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63 -------
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64 masked_alignment : FeatureData[AlignedSequence]
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65 The masked alignment.
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66 ]]>
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67 </help>
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68 </tool>
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